Do you have an example of something you think is horrible? This particular article is extremely technical or "low level," and is beyond what most people would call "music theory," so I wouldn't make too many conclusions just from this article. Most people use "music theory" to refer to music notation systems and some theory about composition, harmony, and rhythm, but seldom diving so deep into the physics and psychology behind interval and pitch perception.
Personally, I find most music terminology to be fairly decent, but I grew up with it, so perhaps I'm the type of person you describe. There is some ambiguity in terminology, some of which is inherent in the dual usage of certain harmonies (is it an A minor 7th flat 5, or a C minor 6th?), and some of which is simply the historical result of competing notations (is it a diminished 7th or a minor 7th flat 5?). However, I think most of the terminology is at least somewhat self-hinting, and the weird random names are few enough to be memorized or looked up when needed (like all the Italian words to notate dynamics and tempo). It certainly doesn't seem particularly worse than the terminology used in, say, computer science or computer programming.
Personally, I find most music terminology to be fairly decent, but I grew up with it, so perhaps I'm the type of person you describe. There is some ambiguity in terminology, some of which is inherent in the dual usage of certain harmonies (is it an A minor 7th flat 5, or a C minor 6th?), and some of which is simply the historical result of competing notations (is it a diminished 7th or a minor 7th flat 5?). However, I think most of the terminology is at least somewhat self-hinting, and the weird random names are few enough to be memorized or looked up when needed (like all the Italian words to notate dynamics and tempo). It certainly doesn't seem particularly worse than the terminology used in, say, computer science or computer programming.